We don't have anything to do this. You could do it in matlab with
read_annotation.m
On 5/15/15 6:44 PM, Andreas Werner wrote:
Dear Experts,
in my analysis i have created a set of surface labels based on
significant clusters using tksurfer.
For a given label I would like to know which
Do you mean by contrasting a condition vs fixation?
Xiaomin
On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve
gr...@nmr.mgh.harvard.edu wrote:
Yes, but you have to set up the contrasts, it won't do it automatically
On 5/16/15 10:48 PM, Xiaomin Yue wrote:
Hi,
During the processing of
hmmm, we distribute strlen.m, not sure why you don't have it. I'll attach
it so you can put it in $FREESURFER_HOME/matlab
cheers
Bruce
On Mon, 18 May 2015, LiuKai
wrote:
Ok, I ve figured it out: the strlen in the code is not a matlab function.
Thus I deleted the lines 38-46, then it
Hi Annie,
Can you share with us how you resolved the issue, so that other people
who might search the email list for similar issues might benefit?
Thanks,
Thomas
On Mon, May 18, 2015 at 3:39 PM, 陳昱潔 poohann1...@gmail.com wrote:
Hi Dr. Yeo:
Thank you very much we already solved the problem!
that means that the version of 3dvolreg.afni does not match your
operating system. What is your OS and what version of FS are you running?
On 5/18/15 4:11 AM, Thục Trinh wrote:
Hi freesurfer experts,
I am practicing on the fsfast tutorial data that were given at
Freesurfer website.
I run the
Hi freesurfer experts,
I am practicing on the fsfast tutorial data that were given at Freesurfer
website.
I run the command to do the pre-processing on the sess01 *noproc*.
*preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -fwhm 5
-per-run*
it was unfinished and failed with the
Ok, I ve figured it out: the strlen in the code is not a matlab function.
Thus I deleted the lines 38-46, then it works well by just define the fname.
Thank you very much!!
kai
From: li...@hotmail.com
To: freesurfer@nmr.mgh.harvard.edu
Subject: RE: Freesurfer Digest, Vol 135, Issue 23
Date: Sun,
yes
On 5/18/15 10:38 AM, Xiaomin Yue wrote:
Do you mean by contrasting a condition vs fixation?
Xiaomin
On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Yes, but you have to set up the contrasts, it won't do it
Dear Douglas Greve,
thank you for your answer. read_annotation gives me the correspondence between anatomical labels and vertices.
To match the vertices to an anatomical region, all i need now (I guess) is a routine to load the vertices in label files as created in tksurfer into matlab.
Is
Thanks
Xiaomin
On Mon, May 18, 2015 at 9:15 AM -0700, Douglas Greve
gr...@nmr.mgh.harvard.edu wrote:
yes
On 5/18/15 10:38 AM, Xiaomin Yue wrote:
Do you mean by contrasting a condition vs fixation?
Xiaomin
On Mon, May 18, 2015 at 7:07 AM -0700, Douglas Greve
Dear Freesurfer experts,
I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs
based on white matter regions as derived in the wmparc.mgz file. I thought of
using the fsaverage subject, but it does not have the
wmparc.mgz file; thus I plan to use the CVS atlas
Hello,
I am getting an error when I try to use the Analyze feature in the Design
tab of Qdec.
The error is:
Error in Analyze: Couldn't open file
/personal_path_to_file/FREESUFER_SUBJECTS/106966-100/surf/lh.thickness.fwhm10.fsaverage.mgz
or .mgh file
However, when I go into the 106966-100
Hi Freesurfers,
I ran recon-all and didn't initially get an error. I am not plotting the
surface in matlab and am getting an error but am not sure why. Any help would
be great! Thanks!
1) BW30
2) recon-all -autorecon1 -autorecon2 -autorecon3 -subject BW30_SurferOutput -i
Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a
combi of tcl and bash I have
almost got my machinery working to make my movies. Just one little fly in the
ointment, it keeps
putting up one after another tksurfer invocation piled on top the last. I have
tried killing
Awesome thank you! Just found out this patient had a previous resection.
Thanks again!
On May 18, 2015, at 4:23 PM, Nick Schmansky, MGH
ni...@nmr.mgh.harvard.edu wrote:
Mia,
Hi, what sort of error? I looked at the image in freeview, and it looks
like the patient is missing their
Hi Greg
put exit at the end of your tcl script and it will quit tksurfer
cheers
Bruce
On Mon, 18 May 2015, Gregory Kirk wrote:
Hi Bruce directed me to the tcl scripting stuff for tksurfer and so with a
combi of tcl and bash I have
almost got my machinery working to make my movies. Just
Mia,
Hi, what sort of error? I looked at the image in freeview, and it looks
like the patient is missing their left frontal lobe. The surfaces look
ok in that region given that.
btw, to make viewing in freeview easy, add this to your .cshrc, all one
line:
alias fv freeview -v mri/T1.mgz
Hello FreeSurfer Experts,
I want to zero out all those voxels from my T1 MRI which are not part of
the cortex preferably in the native space.
I have run the recon-all on the subject.
Any help will be great.
Thanks
Mohammed Goryawala, PhD
University of Miami
Miller School of Medicine.
Hi,
This is a repost, hope someone can please comment?
Thanks.
On Wed, 06 May 2015 00:07:17 -0700 prasser lt;pras...@zoho.comgt; wrote
Thanks Martin. The concern I have with using -autorecon2-cp -autorecon3 after
-surfsegedit is that, new surfaces are created during
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